MS Word's Clippy suddenly taking a level in badass might seem out of nowhere, if not for the Rule of Cool. However, it could also be considered that Clippy had always known how to fight, probably to the point where it was the only thing he was ever good at, hence how awkward and useless he is at trying to help you in the non-fighting department.
The Second Coming's instant knowledge and speed of crafting in vs. Minecraft may look like it came out of nowhere, but in the fourth installment, recall that he made a working ray gun out of Flash's tool icons, and he did it rather quickly.
In part 4, there appears to be an Esoteric Happy Ending going on when you consider the Animator still has to explain that the Facebook shenanigans weren't his fault. On the surface, it seemed doomed to be a Cassandra Truth, and it would be in our world. However, he's talking about what happened in 3 with a friend completely casually and the friend doesn't show any signs of disbelief. And in 2 he also chatted with programmer021 asking for help to defeat a stick figure. Combine this with the side-ad about stick figure enslavement in 3 and it's entirely possible that stick figures coming to life is a semi-regular occurrence, which would make the Animator's alibi more believable. In addition, now that he and the Second Coming are friends, the latter could have just decided to show himself and own up to the deeds.
In "The Rediscovery", everyone maintains the specific interests and skills in Minecraft that they had in "vs. Minecraft". Why does Red's schtick appear to be spawning mobs? Because that's what he was doing for most of "vs. Minecraft" while he was Brainwashed and Crazy; It wasn't until the very end that the others fought him directly—until then they were fighting the hostile mobs he was spawning.
Green was established in the original "vs. Minecraft" to be a very skilled builder, managing to build a functional windmill as soon as he gets his hands on the Minecraft icon, something which can't be done in Vanilla Minecraft without extensive use of command blocks. With this in mind, despite a rough start, him winning the titular competition in "The Building Contest" becomes a Foregone Conclusion.
Liking a Facebook post usually means you agree with the person in what they said. This adds a bit of Alternate Character Interpretation to the stick figure when he likes the "I give up on life" post. Perhaps he too gave up on life, especially since it happens just after his friends die.
When Red starts scrolling through the inventory in "The Rediscovery" in a similar manner to how Possessed!Red did in "Vs. Minecraft", Yellow immediately reaches for the button to activate the arrow dispensers. The Second Coming stops him, and Red is later revealed to just be faking them out, but that prank almost got him shot and killed.
At one point in "Command Blocks", after the blocks start malfunctioning, Green is running around with chickens spawning rapidly from his head. Imagine what that must feel like...